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      Environmental Surveillance as a Tool for Identifying High-risk Settings for Typhoid Transmission

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          Abstract

          Enteric fever remains a major cause of morbidity in developing countries with poor sanitation conditions that enable fecal contamination of water distribution systems. Historical evidence has shown that contamination of water systems used for household consumption or agriculture are key transmission routes for Salmonella Typhi and Salmonella Paratyphi A. The World Health Organization now recommends that typhoid conjugate vaccines (TCV) be used in settings with high typhoid incidence; consequently, governments face a challenge regarding how to prioritize typhoid against other emerging diseases. A key issue is the lack of typhoid burden data in many low- and middle-income countries where TCV could be deployed. Here we present an argument for utilizing environmental sampling for the surveillance of enteric fever organisms to provide data on community-level typhoid risk. Such an approach could complement traditional blood culture-based surveillance or even replace it in settings where population-based clinical surveillance is not feasible. We review historical studies characterizing the transmission of enteric fever organisms through sewage and water, discuss recent advances in the molecular detection of typhoidal Salmonella in the environment, and outline challenges and knowledge gaps that need to be addressed to establish environmental sampling as a tool for generating actionable data that can inform public health responses to enteric fever.

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          Most cited references38

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          Emergence of an Extensively Drug-Resistant Salmonella enterica Serovar Typhi Clone Harboring a Promiscuous Plasmid Encoding Resistance to Fluoroquinolones and Third-Generation Cephalosporins

          ABSTRACT Antibiotic resistance is a major problem in Salmonella enterica serovar Typhi, the causative agent of typhoid. Multidrug-resistant (MDR) isolates are prevalent in parts of Asia and Africa and are often associated with the dominant H58 haplotype. Reduced susceptibility to fluoroquinolones is also widespread, and sporadic cases of resistance to third-generation cephalosporins or azithromycin have also been reported. Here, we report the first large-scale emergence and spread of a novel S. Typhi clone harboring resistance to three first-line drugs (chloramphenicol, ampicillin, and trimethoprim-sulfamethoxazole) as well as fluoroquinolones and third-generation cephalosporins in Sindh, Pakistan, which we classify as extensively drug resistant (XDR). Over 300 XDR typhoid cases have emerged in Sindh, Pakistan, since November 2016. Additionally, a single case of travel-associated XDR typhoid has recently been identified in the United Kingdom. Whole-genome sequencing of over 80 of the XDR isolates revealed remarkable genetic clonality and sequence conservation, identified a large number of resistance determinants, and showed that these isolates were of haplotype H58. The XDR S. Typhi clone encodes a chromosomally located resistance region and harbors a plasmid encoding additional resistance elements, including the bla CTX-M-15 extended-spectrum β-lactamase, and carrying the qnrS fluoroquinolone resistance gene. This antibiotic resistance-associated IncY plasmid exhibited high sequence identity to plasmids found in other enteric bacteria isolated from widely distributed geographic locations. This study highlights three concerning problems: the receding antibiotic arsenal for typhoid treatment, the ability of S. Typhi to transform from MDR to XDR in a single step by acquisition of a plasmid, and the ability of XDR clones to spread globally.
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            Environmental surveillance for polioviruses in the Global Polio Eradication Initiative.

            This article summarizes the status of environmental surveillance (ES) used by the Global Polio Eradication Initiative, provides the rationale for ES, gives examples of ES methods and findings, and summarizes how these data are used to achieve poliovirus eradication. ES complements clinical acute flaccid paralysis (AFP) surveillance for possible polio cases. ES detects poliovirus circulation in environmental sewage and is used to monitor transmission in communities. If detected, the genetic sequences of polioviruses isolated from ES are compared with those of isolates from clinical cases to evaluate the relationships among viruses. To evaluate poliovirus transmission, ES programs must be developed in a manner that is sensitive, with sufficiently frequent sampling, appropriate isolation methods, and specifically targeted sampling sites in locations at highest risk for poliovirus transmission. After poliovirus ceased to be detected in human cases, ES documented the absence of endemic WPV transmission and detected imported WPV. ES provides valuable information, particularly in high-density populations where AFP surveillance is of poor quality, persistent virus circulation is suspected, or frequent virus reintroduction is perceived. Given the benefits of ES, GPEI plans to continue and expand ES as part of its strategic plan and as a supplement to AFP surveillance.
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              Dead or alive: molecular assessment of microbial viability.

              Nucleic acid-based analytical methods, ranging from species-targeted PCRs to metagenomics, have greatly expanded our understanding of microbiological diversity in natural samples. However, these methods provide only limited information on the activities and physiological states of microorganisms in samples. Even the most fundamental physiological state, viability, cannot be assessed cross-sectionally by standard DNA-targeted methods such as PCR. New PCR-based strategies, collectively called molecular viability analyses, have been developed that differentiate nucleic acids associated with viable cells from those associated with inactivated cells. In order to maximize the utility of these methods and to correctly interpret results, it is necessary to consider the physiological diversity of life and death in the microbial world. This article reviews molecular viability analysis in that context and discusses future opportunities for these strategies in genetic, metagenomic, and single-cell microbiology. Copyright © 2014, American Society for Microbiology. All Rights Reserved.
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                Author and article information

                Journal
                Clin Infect Dis
                Clin. Infect. Dis
                cid
                Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
                Oxford University Press (US )
                1058-4838
                1537-6591
                15 August 2020
                29 July 2020
                29 July 2020
                : 71
                : Suppl 2 , Global Action for Local Impact: Research and Developments on Typhoid and Other Invasive Salmonelloses
                : S71-S78
                Affiliations
                [1 ] Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine , Stanford, California, USA
                [2 ] Child Health Research Foundation, Department of Microbiology, Dhaka Shishu Hospital , Dhaka, Bangladesh
                [3 ] Dhulikhel Hospital, Kathmandu University Hospital , Dhulikhel, Nepal
                [4 ] Department of Pediatrics and Child Health, Aga Khan University Hospital Karachi , Karachi, Pakistan
                [5 ] Sabin Vaccine Institute , Washington, DC, USA
                [6 ] Department of Medicine, Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID) University of Cambridge , Cambridge, United Kingdom
                Author notes
                Correspondence: J. R. Andrews, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, 300 Pasteur Dr, Lane Bldg, Ste 143, Rm 141, Stanford, CA 94305 ( jandr@ 123456stanford.edu ).
                Author information
                http://orcid.org/0000-0002-5967-251X
                Article
                ciaa513
                10.1093/cid/ciaa513
                7446943
                32725227
                eeebf8bc-5562-4940-87be-4c4e1655f425
                © The Author(s) 2020. Published by Oxford University Press for the Infectious Diseases Society of America.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 29 July 2020
                Page count
                Pages: 8
                Funding
                Funded by: Bill and Melinda Gates Foundation, DOI 10.13039/100000865;
                Award ID: INV-000572
                Award ID: OPP1113007
                Funded by: Stanford University Center for Innovation in Global Health, DOI 10.13039/100014496;
                Categories
                Supplement Articles
                Novel Tools for Detection of Enteric Fever
                AcademicSubjects/MED00290

                Infectious disease & Microbiology
                typhoid,enteric fever,salmonella,water,environment
                Infectious disease & Microbiology
                typhoid, enteric fever, salmonella, water, environment

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